Package org.sbml.jsbml.ext.qual

Class FunctionTerm

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

org.sbml.jsbml.ext.qual.FunctionTerm

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, MathContainer, SBase, SBaseWithDerivedUnit, TreeNodeWithChangeSupport

public class FunctionTerm
extends AbstractMathContainer

Each FunctionTerm is also associated with a result and in addition to a Boolean function inside a Math element that can be used to set the conditions under which this term is selected.

Since:

1.0

Author:

Nicolas Rodriguez, Finja Büchel, Florian Mittag

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor	Description
FunctionTerm()	Creates a new FunctionTerm instance.
FunctionTerm(int level, int version)	Creates a new FunctionTerm instance.
FunctionTerm(ASTNode math, int level, int version)	Creates a new FunctionTerm instance.
FunctionTerm(FunctionTerm ft)	Creates a FunctionTerm instance from a given FunctionTerm.

Method Summary

Modifier and Type	Method	Description
FunctionTerm	clone()
boolean	equals(java.lang.Object object)
int	getResultLevel()	Returns the resultLevel if it is set, otherwise throw a PropertyUndefinedError Exception.
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isDefaultTerm()	Returns true if it is a defaultTerm.
boolean	isResultLevelMandatory()	Returns false, resultLevel is not mandatory.
boolean	isSetResultLevel()	Returns true if resultLevel is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	setDefaultTerm(boolean defaultTerm)	Sets if this FunctionTerm is a defaultTerm.
void	setResultLevel(int resultLevel)	The result of a term is described by a resultLevel.
boolean	unsetResultLevel()	Unsets the resultLevel.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractMathContainer

containsUndeclaredUnits, getAllowsChildren, getChildAt, getChildCount, getDerivedUnitDefinition, getDerivedUnits, getFormula, getMath, getMathMLString, isSetMath, setFormula, setMath, unsetFormula, unsetMath

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Constructor Detail

FunctionTerm

public FunctionTerm()

Creates a new FunctionTerm instance.

FunctionTerm

public FunctionTerm(int level,
                    int version)

Creates a new FunctionTerm instance.

Parameters:

level - the SBML level

version - the SBML version

FunctionTerm

public FunctionTerm(ASTNode math,
                    int level,
                    int version)

Creates a new FunctionTerm instance.

Parameters:

math - the ASTNode representing the function.

level - the SBML level

version - the SBML version

FunctionTerm

public FunctionTerm(FunctionTerm ft)

Creates a FunctionTerm instance from a given FunctionTerm.

Parameters:

ft - an FunctionTerm object to clone

Method Detail

clone

public FunctionTerm clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractMathContainer

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isResultLevelMandatory

public boolean isResultLevelMandatory()

Returns false, resultLevel is not mandatory.

Returns:

false

isSetResultLevel

public boolean isSetResultLevel()

Returns true if resultLevel is set.

Returns:

true if resultLevel is set.

getResultLevel

public int getResultLevel()

Returns the resultLevel if it is set, otherwise throw a PropertyUndefinedError Exception.

Returns:

the resultLevel if it is set.

Throws:

PropertyUndefinedError - is isSetResultLevel() return false.

setResultLevel

public void setResultLevel(int resultLevel)

The result of a term is described by a resultLevel. This attribute is required. The resultLevel is a non-negative integer describing a level. The resultLevel is used; possibly together with the thresholdLevel or outputLevel to determine the level of a QualitativeSpecies resulting from the Transition.

Parameters:

resultLevel - the resultLevel to set

unsetResultLevel

public boolean unsetResultLevel()

Unsets the resultLevel.

Returns:

true is the resultLevel was set beforehand.

equals

public boolean equals(java.lang.Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

isDefaultTerm

public boolean isDefaultTerm()

Returns true if it is a defaultTerm.

Returns:

true if it is a defaultTerm.

setDefaultTerm

public void setDefaultTerm(boolean defaultTerm)

Sets if this FunctionTerm is a defaultTerm. The defaultTerm defines the default result of a Transition. This term is used if there are no other FunctionTerm elements or if none of the Math elements of the FunctionTerm elements evaluates to "true".

Parameters:

defaultTerm - the defaultTerm to set

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractMathContainer

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractMathContainer